dke-questions
dke-questions > DKE Tractography Error
Sep 14, 2015 09:09 PM | Luis Zertuche
DKE Tractography Error
Hello All,
I get an error using the DKE_FT tool that I can't figure out how to solve. Message reads:
C:\Users\luis\Desktop\DKE_FIBERTRACKING>dke_ft.exe ft_parameters.txt
Starting matlabpool using the 'local' profile ... connected to 2 labs.
Start date and time: September 14, 2015 14:53:54
Fiber Tractography with DKI version 1
July 2015
Optimizing kurtosis dODF...Error using dke_ft (line 132)
The number of voxels in the FA image and the tensors must match!
Make sure map_interpolation_method.flag = 0 for tensor fitting or reconstruct
the fa image from the DT.mat using the Nifti header from the diffusion weighted
images.
Does this mean I have re-run the preprocessing again unchecking the interpolation flag in the gui? (took 5 hours to run)
~Thanks for the help, Luis.
PS
My scanner (Siemens Skyra) puts out a FA map (and and FA colored map) for the DKI run, is there a way I could use that to skip some of the preprocessing or do tractography on that one directly?
Ps 2
This is the parameters file that I used for preprocessing with DKE:
% Wed Sep 09 05:12:24 PM
studydir = 'C:\Users\luis\Desktop\S8306TYX_126265_3\cmrr009DKI_64dir2x2x2';
subject_list = {''};
preprocess_options.format = 'dicom';
preprocess_options.navg = 1;
preprocess_options.extra_b0 = 0;
preprocess_options.coreg_flag = 1;
preprocess_options.series_description = {'cmrr009DKI_64dir2x2x2'};
fn_img_prefix = 'rdki';
bval = [0 1000 2000];
ndir = 64;
idx_1st_img = 1;
Kmin = 0;
NKmax = 3;
Kmin_final = 0;
Kmax_final = 3;
T = 50;
find_brain_mask_flag = 1;
dki_method.no_tensor = 0;
dki_method.linear_weighting = 1;
dki_method.linear_constrained = 1;
dki_method.nonlinear = 0;
dki_method.linear_violations = 0;
dki_method.robust_option = 0;
dki_method.noise_tolerance = 0.09;
dti_method.dti_flag = 0;
dti_method.dti_only = 0;
dti_method.no_tensor = 0;
dti_method.linear_weighting = 1;
dti_method.b_value = 1e+003;
dti_method.directions{1} = [1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64];
dti_method.robust_option = 0;
dti_method.noise_tolerance = 0.09;
fn_noise = '';
fwhm_img = [3.375 3.375 3.375];
fwhm_noise = [0 0 0];
median_filter_method = 2;
map_interpolation_method.flag = 1;
map_interpolation_method.order = 1;
map_interpolation_method.resolution = 1;
fn_gradients = 'C:/Users/luis/Desktop/S8306TYX_126265_3/bvec_64dir_b0rem.txt';
idx_gradients{1} = [1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64];
idx_gradients{2} = [1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64];
I get an error using the DKE_FT tool that I can't figure out how to solve. Message reads:
C:\Users\luis\Desktop\DKE_FIBERTRACKING>dke_ft.exe ft_parameters.txt
Starting matlabpool using the 'local' profile ... connected to 2 labs.
Start date and time: September 14, 2015 14:53:54
Fiber Tractography with DKI version 1
July 2015
Optimizing kurtosis dODF...Error using dke_ft (line 132)
The number of voxels in the FA image and the tensors must match!
Make sure map_interpolation_method.flag = 0 for tensor fitting or reconstruct
the fa image from the DT.mat using the Nifti header from the diffusion weighted
images.
Does this mean I have re-run the preprocessing again unchecking the interpolation flag in the gui? (took 5 hours to run)
~Thanks for the help, Luis.
PS
My scanner (Siemens Skyra) puts out a FA map (and and FA colored map) for the DKI run, is there a way I could use that to skip some of the preprocessing or do tractography on that one directly?
Ps 2
This is the parameters file that I used for preprocessing with DKE:
% Wed Sep 09 05:12:24 PM
studydir = 'C:\Users\luis\Desktop\S8306TYX_126265_3\cmrr009DKI_64dir2x2x2';
subject_list = {''};
preprocess_options.format = 'dicom';
preprocess_options.navg = 1;
preprocess_options.extra_b0 = 0;
preprocess_options.coreg_flag = 1;
preprocess_options.series_description = {'cmrr009DKI_64dir2x2x2'};
fn_img_prefix = 'rdki';
bval = [0 1000 2000];
ndir = 64;
idx_1st_img = 1;
Kmin = 0;
NKmax = 3;
Kmin_final = 0;
Kmax_final = 3;
T = 50;
find_brain_mask_flag = 1;
dki_method.no_tensor = 0;
dki_method.linear_weighting = 1;
dki_method.linear_constrained = 1;
dki_method.nonlinear = 0;
dki_method.linear_violations = 0;
dki_method.robust_option = 0;
dki_method.noise_tolerance = 0.09;
dti_method.dti_flag = 0;
dti_method.dti_only = 0;
dti_method.no_tensor = 0;
dti_method.linear_weighting = 1;
dti_method.b_value = 1e+003;
dti_method.directions{1} = [1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64];
dti_method.robust_option = 0;
dti_method.noise_tolerance = 0.09;
fn_noise = '';
fwhm_img = [3.375 3.375 3.375];
fwhm_noise = [0 0 0];
median_filter_method = 2;
map_interpolation_method.flag = 1;
map_interpolation_method.order = 1;
map_interpolation_method.resolution = 1;
fn_gradients = 'C:/Users/luis/Desktop/S8306TYX_126265_3/bvec_64dir_b0rem.txt';
idx_gradients{1} = [1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64];
idx_gradients{2} = [1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64];
Threaded View
Title | Author | Date |
---|---|---|
Luis Zertuche | Sep 14, 2015 | |
qianrunda | May 12, 2019 | |
Xinman Liu | Apr 11, 2018 | |
Russell Glenn | Sep 15, 2015 | |
sevim sahin | Dec 7, 2016 | |
Emilie McKinnon | Dec 12, 2016 | |